Feature request: disable cloud MCP integrations per-project

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Hi,

I'm using Claude Code with several cloud MCP integrations connected to my Claude account (Slack, Notion, Make, Miro, Circleback, Google Drive, Stripe, Supabase). These are useful across different contexts, but in specific projects I only need 2 of them (Stripe and Supabase).

The problem is that all ~150 deferred tool definitions from unused integrations are loaded into every conversation's context window, consuming an estimated 15-25% of available context before I even type my first message. This significantly reduces the effective context I have for actual work — especially when using subagents, which compound the issue.

Current behavior: Cloud MCP integrations (mcp__claude_ai_*) load globally in all sessions. There is no way to disable them per-project.

Requested behavior: Support a disabledMcpServers key (or similar) in .claude/settings.json at the project level that allows disabling specific cloud integrations. Example:

{
"disabledMcpServers": ["Slack", "Notion", "Make", "Miro", "Circleback", "Google_Drive"]
}
This would let developers keep integrations connected globally while only loading what's relevant per-project, optimizing context usage.

Thank you for considering this.

What Should Happen?

Cloud MCP integrations (mcp__claude_ai_*) should be configurable per-project. A disabledMcpServers key in .claude/settings.json should allow disabling specific cloud integrations at the project level. Example:

{
"disabledMcpServers": ["Slack", "Notion", "Make", "Miro", "Circleback", "Google_Drive"]
}

This way, developers can keep integrations connected globally but only load the ones relevant to each project, saving 15-25% of context window that is currently wasted on ~150 unused deferred tool definitions.

Error Messages/Logs

Steps to Reproduce

1. Connect multiple cloud MCP integrations to your Claude account (e.g., Slack, Notion, Make, Miro, Circleback, Google Drive, Stripe, Supabase)
2. Open Claude Code in a project that only needs 2 of them (e.g., Stripe + Supabase)
3. Observe that all ~150 deferred tool definitions from ALL integrations are loaded into the conversation context
4. There is no setting in .claude/settings.json or .claude/settings.local.json to disable specific cloud integrations per-project

Result: ~15-25% of the context window is consumed by unused tool definitions before the user sends their first message.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.120 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_